Uses of Class
de.isas.mztab2.model.Metadata

Packages that use Metadata

Package	Description
de.isas.mztab2.io.serialization	This package contains classes that implement custom Jackson serializers for the mzTab-M model objects.
de.isas.mztab2.io.validators	This package contains implementations for validation of mzTab-M parts during parsing.
de.isas.mztab2.model	Base package for the jmztab-m data model, generated from the mzTab_m_swagger.yml specification.
uk.ac.ebi.pride.jmztab2.model	This package contains model classes for mzTab-M structural features like mandatory and optional columns.
uk.ac.ebi.pride.jmztab2.utils.parser	This package contains text file line parser implementations for the mzTab-M document sections.

Uses of Metadata in de.isas.mztab2.io.serialization

Methods in de.isas.mztab2.io.serialization with parameters of type Metadata

Modifier and Type	Method	Description
void	MetadataSerializer.serialize(Metadata t, com.fasterxml.jackson.core.JsonGenerator jg, com.fasterxml.jackson.databind.SerializerProvider sp)

Constructor parameters in de.isas.mztab2.io.serialization with type arguments of type Metadata

Constructor	Description
MetadataSerializer(Class<Metadata> t)	Constructor for MetadataSerializer.

Uses of Metadata in de.isas.mztab2.io.validators

Methods in de.isas.mztab2.io.validators with parameters of type Metadata

Modifier and Type	Method	Description
List<MZTabError>	AssayValidator.validateRefine(Metadata metadata, MZTabParserContext parserContext)
List<MZTabError>	CvValidator.validateRefine(Metadata metadata, MZTabParserContext parserContext)
List<MZTabError>	DatabaseValidator.validateRefine(Metadata metadata, MZTabParserContext parserContext)
List<MZTabError>	MsRunValidator.validateRefine(Metadata metadata, MZTabParserContext parserContext)
List<MZTabError>	MzTabIdValidator.validateRefine(Metadata metadata, MZTabParserContext parserContext)
List<MZTabError>	MzTabVersionValidator.validateRefine(Metadata metadata, MZTabParserContext parserContext)
List<MZTabError>	QuantificationMethodValidator.validateRefine(Metadata metadata, MZTabParserContext parserContext)
List<MZTabError>	SmallMoleculeFeatureQuantificationUnitValidator.validateRefine(Metadata metadata, MZTabParserContext parserContext)
List<MZTabError>	SmallMoleculeIdConfidenceMeasureValidator.validateRefine(Metadata metadata, MZTabParserContext parserContext)
List<MZTabError>	SmallMoleculeQuantificationUnitValidator.validateRefine(Metadata metadata, MZTabParserContext parserContext)
List<MZTabError>	SoftwareValidator.validateRefine(Metadata metadata, MZTabParserContext parserContext)
List<MZTabError>	StudyVariableValidator.validateRefine(Metadata metadata, MZTabParserContext parserContext)

Uses of Metadata in de.isas.mztab2.model

Methods in de.isas.mztab2.model that return Metadata

Modifier and Type	Method	Description
Metadata	Metadata.addAssayItem(Assay assayItem)	Add a single assayItem to the assay collection.
Metadata	Metadata.addColunitSmallMoleculeEvidenceItem(ColumnParameterMapping colunitSmallMoleculeEvidenceItem)	Add a single colunitSmallMoleculeEvidenceItem to the colunitSmallMoleculeEvidence collection.
Metadata	Metadata.addColunitSmallMoleculeFeatureItem(ColumnParameterMapping colunitSmallMoleculeFeatureItem)	Add a single colunitSmallMoleculeFeatureItem to the colunitSmallMoleculeFeature collection.
Metadata	Metadata.addColunitSmallMoleculeItem(ColumnParameterMapping colunitSmallMoleculeItem)	Add a single colunitSmallMoleculeItem to the colunitSmallMolecule collection.
Metadata	Metadata.addContactItem(Contact contactItem)	Add a single contactItem to the contact collection.
Metadata	Metadata.addCustomItem(Parameter customItem)	Add a single customItem to the custom collection.
Metadata	Metadata.addCvItem(CV cvItem)	Add a single cvItem to the cv collection.
Metadata	Metadata.addDatabaseItem(Database databaseItem)	Add a single databaseItem to the database collection.
Metadata	Metadata.addDerivatizationAgentItem(Parameter derivatizationAgentItem)	Add a single derivatizationAgentItem to the derivatizationAgent collection.
Metadata	Metadata.addExternalStudyUriItem(Uri externalStudyUriItem)	Add a single externalStudyUriItem to the externalStudyUri collection.
Metadata	Metadata.addIdConfidenceMeasureItem(Parameter idConfidenceMeasureItem)	Add a single idConfidenceMeasureItem to the idConfidenceMeasure collection.
Metadata	Metadata.addInstrumentItem(Instrument instrumentItem)	Add a single instrumentItem to the instrument collection.
Metadata	Metadata.addMsRunItem(MsRun msRunItem)	Add a single msRunItem to the msRun collection.
Metadata	Metadata.addPublicationItem(Publication publicationItem)	Add a single publicationItem to the publication collection.
Metadata	Metadata.addSampleItem(Sample sampleItem)	Add a single sampleItem to the sample collection.
Metadata	Metadata.addSampleProcessingItem(SampleProcessing sampleProcessingItem)	Add a single sampleProcessingItem to the sampleProcessing collection.
Metadata	Metadata.addSoftwareItem(Software softwareItem)	Add a single softwareItem to the software collection.
Metadata	Metadata.addStudyVariableItem(StudyVariable studyVariableItem)	Add a single studyVariableItem to the studyVariable collection.
Metadata	Metadata.addUriItem(Uri uriItem)	Add a single uriItem to the uri collection.
Metadata	Metadata.assay(List<Assay> assay)	Builder method for assay.
Metadata	Metadata.colunitSmallMolecule(List<ColumnParameterMapping> colunitSmallMolecule)	Builder method for colunitSmallMolecule.
Metadata	Metadata.colunitSmallMoleculeEvidence(List<ColumnParameterMapping> colunitSmallMoleculeEvidence)	Builder method for colunitSmallMoleculeEvidence.
Metadata	Metadata.colunitSmallMoleculeFeature(List<ColumnParameterMapping> colunitSmallMoleculeFeature)	Builder method for colunitSmallMoleculeFeature.
Metadata	Metadata.contact(List<Contact> contact)	Builder method for contact.
Metadata	Metadata.custom(List<Parameter> custom)	Builder method for custom.
Metadata	Metadata.cv(List<CV> cv)	Builder method for cv.
Metadata	Metadata.database(List<Database> database)	Builder method for database.
Metadata	Metadata.derivatizationAgent(List<Parameter> derivatizationAgent)	Builder method for derivatizationAgent.
Metadata	Metadata.description(String description)	Builder method for description.
Metadata	Metadata.externalStudyUri(List<Uri> externalStudyUri)	Builder method for externalStudyUri.
@NotNull @Valid Metadata	MzTab.getMetadata()	Get metadata.
Metadata	Metadata.idConfidenceMeasure(List<Parameter> idConfidenceMeasure)	Builder method for idConfidenceMeasure.
Metadata	Metadata.instrument(List<Instrument> instrument)	Builder method for instrument.
Metadata	Metadata.msRun(List<MsRun> msRun)	Builder method for msRun.
Metadata	Metadata.mzTabID(String mzTabID)	Builder method for mzTabID.
Metadata	Metadata.mzTabVersion(String mzTabVersion)	Builder method for mzTabVersion.
Metadata	Metadata.prefix(Metadata.PrefixEnum prefix)	Builder method for prefix.
Metadata	Metadata.publication(List<Publication> publication)	Builder method for publication.
Metadata	Metadata.quantificationMethod(Parameter quantificationMethod)	Builder method for quantificationMethod.
Metadata	Metadata.sample(List<Sample> sample)	Builder method for sample.
Metadata	Metadata.sampleProcessing(List<SampleProcessing> sampleProcessing)	Builder method for sampleProcessing.
Metadata	Metadata.smallMoleculeFeatureQuantificationUnit(Parameter smallMoleculeFeatureQuantificationUnit)	Builder method for smallMoleculeFeatureQuantificationUnit.
Metadata	Metadata.smallMoleculeIdentificationReliability(Parameter smallMoleculeIdentificationReliability)	Builder method for smallMoleculeIdentificationReliability.
Metadata	Metadata.smallMoleculeQuantificationUnit(Parameter smallMoleculeQuantificationUnit)	Builder method for smallMoleculeQuantificationUnit.
Metadata	Metadata.software(List<Software> software)	Builder method for software.
Metadata	Metadata.studyVariable(List<StudyVariable> studyVariable)	Builder method for studyVariable.
Metadata	Metadata.title(String title)	Builder method for title.
Metadata	Metadata.uri(List<Uri> uri)	Builder method for uri.

Methods in de.isas.mztab2.model with parameters of type Metadata

Modifier and Type	Method	Description
Optional<Assay>	MzTabAccess.getAssayFor(OptColumnMapping columnMapping, Metadata metadata)	Tries to locate the assay referenced by id from the columnMapping identifier.
Optional<Assay>	MzTabAccess.getAssayFor(Integer id, Metadata metadata)	Tries to locate the assay referenced by id from the metadata section.
Optional<Database>	MzTabAccess.getDatabaseFor(Integer id, Metadata metadata)	Tries to locate the database referenced by id from the metadata section.
Optional<MsRun>	MzTabAccess.getMsRunFor(Integer id, Metadata metadata)	Tries to locate the ms run referenced by id from the metadata section.
Optional<StudyVariable>	MzTabAccess.getStudyVariableFor(Integer id, Metadata metadata)	Tries to locate the study variable referenced by id from the metadata section.
MzTab	MzTab.metadata(Metadata metadata)	Builder method for metadata.
void	MzTab.setMetadata(Metadata metadata)	Set metadata.

Uses of Metadata in uk.ac.ebi.pride.jmztab2.model

Methods in uk.ac.ebi.pride.jmztab2.model with parameters of type Metadata

Modifier and Type	Method	Description
static List<SpectraRef>	MZTabUtils.parseSpectraRefList(MZTabParserContext context, Metadata metadata, String target)	Parse a SpectraRef list.

Uses of Metadata in uk.ac.ebi.pride.jmztab2.utils.parser

Fields in uk.ac.ebi.pride.jmztab2.utils.parser declared as Metadata

Modifier and Type	Field	Description
protected Metadata	MZTabDataLineParser.metadata
protected Metadata	MZTabHeaderLineParser.metadata

Methods in uk.ac.ebi.pride.jmztab2.utils.parser that return Metadata

Modifier and Type	Method	Description
Metadata	MTDLineParser.getMetadata()	Getter for the field metadata.

Methods in uk.ac.ebi.pride.jmztab2.utils.parser with parameters of type Metadata

Modifier and Type	Method	Description
Assay	MZTabParserContext.addAssay(Metadata metadata, Assay assay)	Add a assay into metadata.
Assay	MZTabParserContext.addAssayCustom(Metadata metadata, Integer id, Parameter param)	Add a assay[id]-custom[i] into metadata.
Assay	MZTabParserContext.addAssayExternalUri(Metadata metadata, Integer id, URI location)	Add a assay[id]-external_uri into metadata.
Assay	MZTabParserContext.addAssayMsRun(Metadata metadata, Integer id, MsRun msRun)	Add assay[id]-ms_run_ref into metadata.
Assay	MZTabParserContext.addAssaySample(Metadata metadata, Integer id, Sample sample)	Add assay[id]-sample_ref into metadata.
Contact	MZTabParserContext.addContact(Metadata metadata, Contact contact)	Add a contact into metadata.
Contact	MZTabParserContext.addContactAffiliation(Metadata metadata, Integer id, String affiliation)	Add contact[id]-affiliation.
Contact	MZTabParserContext.addContactEmail(Metadata metadata, Integer id, String email)	Add contact[id]-email
Contact	MZTabParserContext.addContactName(Metadata metadata, Integer id, String name)	Add contact[id]-name.
CV	MZTabParserContext.addCV(Metadata metadata, CV cv)	Add a controlled vocabularies/ontologies into metadata.
CV	MZTabParserContext.addCVFullName(Metadata metadata, Integer id, String fullName)	Add a cv[id]-full_name.
CV	MZTabParserContext.addCVLabel(Metadata metadata, Integer id, String label)	Add a cv[id]-label.
CV	MZTabParserContext.addCVURI(Metadata metadata, Integer id, String uri)	Add a cv[id]-uri.
CV	MZTabParserContext.addCVVersion(Metadata metadata, Integer id, String version)	Add a cv[id]-version.
Database	MZTabParserContext.addDatabase(Metadata metadata, Database database)	addDatabase.
Database	MZTabParserContext.addDatabasePrefix(Metadata metadata, Integer id, String valueLabel)	addDatabasePrefix.
Database	MZTabParserContext.addDatabaseUri(Metadata metadata, Integer id, URI checkURI)	addDatabaseUri.
Database	MZTabParserContext.addDatabaseVersion(Metadata metadata, Integer id, String version)	addDatabaseVersion.
Instrument	MZTabParserContext.addInstrument(Metadata metadata, Instrument instrument)	Add a instrument[id] to metadata.
Instrument	MZTabParserContext.addInstrumentAnalyzer(Metadata metadata, Integer id, Parameter analyzer)	Add a parameter for instrument[id]-analyzer[i]
Instrument	MZTabParserContext.addInstrumentDetector(Metadata metadata, Integer id, Parameter detector)	Add a parameter for instrument[id]-detector
Instrument	MZTabParserContext.addInstrumentName(Metadata metadata, Integer id, Parameter name)	Add a parameter for instrument[id]-name
Instrument	MZTabParserContext.addInstrumentSource(Metadata metadata, Integer id, Parameter source)	Add a parameter for instrument[id]-source
MsRun	MZTabParserContext.addMsRun(Metadata metadata, MsRun msRun)	Add a ms_run[id] into metadata.
MsRun	MZTabParserContext.addMsRunFormat(Metadata metadata, Integer id, Parameter format)	Add ms_run[id]-format into metadata.
MsRun	MZTabParserContext.addMsRunFragmentationMethod(Metadata metadata, Integer id, Parameter fragmentationMethod)	Add ms_run[id]-fragmentation_method into metadata.
MsRun	MZTabParserContext.addMsRunHash(Metadata metadata, Integer id, String hash)	addMsRunHash.
MsRun	MZTabParserContext.addMsRunHashMethod(Metadata metadata, Integer id, Parameter hashMethod)	addMsRunHashMethod.
MsRun	MZTabParserContext.addMsRunIdFormat(Metadata metadata, Integer id, Parameter idFormat)	Add ms_run[id]-id_format into metadata.
MsRun	MZTabParserContext.addMsRunInstrumentRef(Metadata metadata, Integer id, Instrument instrument)	Add ms_run[id]-instrument_ref into metadata.
MsRun	MZTabParserContext.addMsRunLocation(Metadata metadata, Integer id, URI location)	Add ms_run[id]-location into metadata.
MsRun	MZTabParserContext.addMsRunScanPolarity(Metadata metadata, Integer id, Parameter scanPolarity)	addMsRunScanPolarity.
Publication	MZTabParserContext.addPublication(Metadata metadata, Publication publication)	Add a publiction to metadata.
Publication	MZTabParserContext.addPublicationItem(Metadata metadata, Integer id, PublicationItem.TypeEnum type, String accession)	Add a publication item to metadata.
Publication	MZTabParserContext.addPublicationItems(Metadata metadata, Integer id, Collection<PublicationItem> items)	Add a couple of publication items into publication[id].
Sample	MZTabParserContext.addSample(Metadata metadata, Sample sample)	Add a sample to metadata.
Sample	MZTabParserContext.addSampleCellType(Metadata metadata, Integer id, Parameter cellType)	Add a sample[id]-cell_type into sample.
Sample	MZTabParserContext.addSampleCustom(Metadata metadata, Integer id, Parameter custom)	Add a sample[id]-custom into sample.
Sample	MZTabParserContext.addSampleDescription(Metadata metadata, Integer id, String description)	Add a sample[id]-description into sample.
Sample	MZTabParserContext.addSampleDisease(Metadata metadata, Integer id, Parameter disease)	Add a sample[id]-disease into sample.
SampleProcessing	MZTabParserContext.addSampleProcessing(Metadata metadata, Integer id, List<Parameter> sampleProcessing)	Add a sample_processing[id].
SampleProcessing	MZTabParserContext.addSampleProcessingParameter(Metadata metadata, Integer id, Parameter param)	Add a processing parameter to sample_processing[id]
Sample	MZTabParserContext.addSampleSpecies(Metadata metadata, Integer id, Parameter species)	Add a sample[id]-species into sample.
Sample	MZTabParserContext.addSampleTissue(Metadata metadata, Integer id, Parameter tissue)	Add a sample[id]-tissue into sample.
void	MZTabParserContext.addSmallMoleculeColUnit(Metadata metadata, String columnName, Parameter param)	Defines the unit for the data reported in a column of the small molecule section.
void	MZTabParserContext.addSmallMoleculeEvidenceColUnit(Metadata metadata, String columnName, Parameter param)	Defines the unit for the data reported in a column of the small molecule section.
void	MZTabParserContext.addSmallMoleculeFeatureColUnit(Metadata metadata, String columnName, Parameter param)	Defines the unit for the data reported in a column of the small molecule section.
Software	MZTabParserContext.addSoftware(Metadata metadata, Software software)	Add a software to metadata, which used to analyze the data and obtain the reported results.
Software	MZTabParserContext.addSoftwareParameter(Metadata metadata, Integer id, Parameter param)	Add a software[id] parameter.
Software	MZTabParserContext.addSoftwareSetting(Metadata metadata, Integer id, String setting)	Add a software[id]-setting.
StudyVariable	MZTabParserContext.addStudyVariable(Metadata metadata, StudyVariable studyVariable)	Add a study variable into metadata.
StudyVariable	MZTabParserContext.addStudyVariableAssay(Metadata metadata, Integer id, Assay assay)	Add a study_variable[id]-assay_refs.
StudyVariable	MZTabParserContext.addStudyVariableAverageFunction(Metadata metadata, Integer id, Parameter checkParameter)	Add a study_variable[id]-average_function.
StudyVariable	MZTabParserContext.addStudyVariableDescription(Metadata metadata, Integer id, String description)	Add a study_variable[id]-description.
StudyVariable	MZTabParserContext.addStudyVariableFactors(Metadata metadata, Integer id, Parameter checkParameter)	Add a study_variable[id]-factor.
StudyVariable	MZTabParserContext.addStudyVariableVariationFunction(Metadata metadata, Integer id, Parameter checkParameter)	Add a study_variable[id]-variation_function.

Constructors in uk.ac.ebi.pride.jmztab2.utils.parser with parameters of type Metadata

Constructor	Description
MZTabDataLineParser(MZTabParserContext context, MZTabColumnFactory factory, PositionMapping positionMapping, Metadata metadata, MZTabErrorList errorList)	Generate a mzTab data line parser.
MZTabHeaderLineParser(MZTabParserContext context, MZTabColumnFactory factory, Metadata metadata)	Parse a header line into MZTabColumnFactory structure.
SEHLineParser(MZTabParserContext context, Metadata metadata)	Constructor for SEHLineParser.
SFHLineParser(MZTabParserContext context, Metadata metadata)	Constructor for SFHLineParser.
SMELineParser(MZTabParserContext context, MZTabColumnFactory factory, PositionMapping positionMapping, Metadata metadata, MZTabErrorList errorList)	Constructor for SMELineParser.
SMFLineParser(MZTabParserContext context, MZTabColumnFactory factory, PositionMapping positionMapping, Metadata metadata, MZTabErrorList errorList)	Constructor for SMFLineParser.
SMHLineParser(MZTabParserContext context, Metadata metadata)	Constructor for SMHLineParser.
SMLLineParser(MZTabParserContext context, MZTabColumnFactory factory, PositionMapping positionMapping, Metadata metadata, MZTabErrorList errorList)	Constructor for SMLLineParser.